analyzeVariants | Calculate and process Variants |
annotateVariants | Annotate variants via vep |
buildGenomicFeaturesFromTxDb | Build genomic features from a TxDb object |
callVariantsGATK | Variant calling via GATK |
checkGATKJar | Check for the GATK jar file |
detectRRNA | Detect rRNA Contamination in Reads |
excludeVariantsByRegions | Filter variants by regions |
gatk | gatk |
generateSingleGeneDERs | generateSingleGeneDERs |
getRRNAIds | Detect reads that look like rRNA |
getTabDataFromFile | Load tabular data from the NGS pipeline result directory |
hashCoverage | Hashing function for coverage |
hashVariants | Hashing function for variants |
hashVector | Hashing function for vector |
HTSeqGenie | Package overview |
isSparse | isSparse |
markDuplicates | markDuplicates |
markDups | markDups |
realignIndels | realignIndels |
realignIndelsGATK | Realign indels via GATK |
runPipeline | Run the NGS analysis pipeline |
runPipelineConfig | Run the NGS analysis pipeline |
setupTestFramework | setup test framework |
TP53GenomicFeatures | Demo genomic features around the TP53 gene |
vcfStat | Compute stats on a VCF file |
wrap.callVariants | Variant calling |
writeVCF | writeVCF |